A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
International Journal of Bioinformatics Research and Applications
RepFrag: a graph based method for finding repeats and transposons from fragmented genomes
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Procrastination leads to efficient filtration for local multiple alignment
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
| Hi-index | 3.84 |
Summary: Repeated elements such as satellites and transposons are ubiquitous in eukaryotic genomes. De novo computational identification and classification of such elements is a challenging problem. Therefore, repeat annotation of sequenced genomes has historically largely relied on sequence similarity to hand-curated libraries of known repeat families. We present a new approach to de novo repeat annotation that exploits characteristic patterns of local alignments induced by certain classes of repeats. We describe PILER, a package of efficient search algorithms for identifying such patterns. Novel repeats found using PILER are reported for Homo sapiens, Arabidopsis thalania and Drosophila melanogaster. Availability: The PILER software is freely available at http://www.drive5.com/piler Contact: bob@drive5.com